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In epigenetics, histone modifications—occurring on the lysine- and arginine-rich N-terminal tails of histones H2A, H2B, H3, and H4—are key regulators of chromatin dynamics and gene expression, encompassing over a dozen post-translational modifications such as methylation, acetylation, phosphorylation, ubiquitination, SUMOylation, and ADP-ribosylation. These modifications not only control transcription, DNA repair, chromosome condensation, and cell cycle progression but also influence disease processes, with specific marks like H3K27ac and H3K4me3 serving as biomarkers and therapeutic targets in cancer, neurodevelopmental disorders, and aging, making comprehensive profiling essential for understanding gene regulation and developing novel therapies.
Figure 1. Histone tail modifications with amino acid positions and color-coded modification types. (Lawrence M, et al., 2016)
Table 1. Common Modification Summary
Activating Marks
Repressive Marks
Structural / Regulatory Marks
| Mark | Functional Role | Notes |
| H2AFZ (H2A.Z) | Activation, increases chromatin accessibility | Promoters, enhancers; may act at boundaries |
| H3F3A (H3.3) | Activation, transcription-dependent deposition | Gene bodies, regulatory regions |
| H2AK4/5ac | Transcriptional activation | H2A tail |
| H2AK7ac | Transcriptional activation | H2A tail |
| H2BS33P | Transcriptional activation | H2B tail |
| H2BK5/11/12/15/16/20ac | Transcriptional activation | H2B tail |
| H2BK123ub | Transcriptional activation | Gene body |
| H3ac (Global H3 acetylation) | Chromatin relaxation; activation | Promoters, enhancers |
| H3K4ac | Transcriptional activation | Promoters |
| H3K9ac | Histone deposition; activation | Promoters, enhancers |
| H3K14ac | Activation; DNA repair | Promoters, enhancers |
| H3K23ac | Activation; DNA repair | Promoters |
| H3K27ac | Active enhancers and promoters | Enhancers, promoters |
| H3K4me1 | Enhancer mark, poised/active | Enhancer regions |
| H3K4me2 | Activation; permissive euchromatin | Promoters, regulatory regions |
| H3K4me3 | Strong activation; active promoters | TSS (sharp peak) |
| H3K36me3 | Activation; transcription elongation | Gene body |
| H3K79me2/3 | Activation; transcription elongation | Gene bodies |
| H2BK120ub (H2Bub1) | Activation; transcription elongation | Gene bodies |
| H3R17me | Transcriptional activation | H3 tail |
| H3S10ph | Activation; transcription, mitosis | Promoters, chromosome arms |
| H4R3me | Transcriptional activation | H4 tail |
| H4K5/8/12/16ac | Activation; DNA repair; histone deposition | Promoters, enhancers, telomeric regions |
| Mark | Functional Role | Notes |
| H2AK119ub / H2AK119P | Repression; Polycomb-mediated silencing / Spermatogenesis | Promoters / germ cells |
| H2BK120ub | Spermatogenesis / meiosis | Gene body |
| H3K9me2/3 | Repression; heterochromatin; imprinting | Pericentromeres, satellite DNA |
| H3K27me3 | Transcriptional silencing; X-inactivation; bivalent domains | Developmental genes, repressed regions |
| H4K20me1/3 | Silencing; heterochromatin | Gene body, repeats |
| SUMOylation (H3/H4) | Mostly repressive; blocks TF binding | Multiple sites |
| Mark | Functional Role | Notes |
| H3T3ph, H3T11ph, H3S28ph | Mitotic/meiotic chromosome regulation | Centromeres, chromosome arms |
| H4K20me1 | DNA replication / repair; structural | Gene bodies, regulatory regions |
| ADP-ribosylation | DNA damage response, stress regulation | Multiple sites |
| H1K18ac | Transcription activation; DNA repair; replication | H1 tail |
| H4S1P | Mitosis | H4 tail |
Leveraging advanced proteomics and epigenetics platforms, Creative Biogene combines high-resolution mass spectrometry, HPLC-based purification, and optimized multi-enzyme digestion strategies to provide highly sensitive and broad-coverage histone modification profiling and quantitative analysis. Unlike conventional proteomic quantification, histone modification analysis requires specialized protocols due to the strong basicity of nuclear proteins and the complexity of PTMs, making workflow optimization critical. Through this platform, we are capable of profiling 16+ types of histone modifications, including but not limited to methylation, acetylation, phosphorylation, ubiquitination, SUMOylation, butyrylation, propionylation, lactylation, succinylation, and glutarylation.
1Histone extraction and purification: Efficient nuclear extraction under acidic or high-salt conditions, followed by centrifugation, buffer precipitation, and HPLC separation to obtain purified histone fractions.
2Sample preparation and optimized digestion: To minimize loss of modification information due to peptide length or ionization efficiency, we employ multiple proteases (e.g., trypsin, Glu-C) for comprehensive digestion and improved MS coverage.
3Mass spectrometry detection and data acquisition: High-resolution MS ensures accurate identification of modification sites and reliable quantification.
4Bioinformatics analysis and interpretation: Our expert bioinformatics team integrates multi-dimensional databases to perform comparative analysis and functional annotation, delivering histone modification distribution maps, relative quantification data, and biological insights.
We support multiple sample types, including tissues, cells, blood, serum, urine, and microbial samples. General requirements are as follows:
| Sample Type | Requirement |
| Tissue | ≥100 mg (plant); ≥2 g (animal) |
| Blood | ≥2 ml (EDTA anticoagulated) |
| Serum / Urine | ≥2 ml (serum); ≥10 ml (urine) |
| Cells | ≥1 × 10⁸ cells |
| Protein Samples | Total protein ≥2–5 mg |
| Microorganisms | ≥400 mg (wet weight or dry weight) |
Note: For detailed requirements or special sample types, please don't hesitate to contact our technical support team for consultation.
All samples should be shipped on sufficient dry ice using express delivery to minimize degradation. Quality assessment will be performed before formal analysis to ensure suitability.
Whether your goal is to generate a comprehensive histone modification atlas or to focus on quantitative analysis of specific modifications, Creative Biogene offers reliable and professional solutions to accelerate your research and drug development. Please feel free to contact our technical support team for a customized service plan tailored to your research needs.
1. Are there established methods for detecting the modification I am interested in?
Most classical modifications (such as acetylation, methylation, phosphorylation, and ubiquitination) have well-validated commercial antibodies and assay kits. For emerging modifications, we can perform mass spectrometry-based detection or assist with custom antibody development.
2. How can I study a novel modification site?
We recommend non-targeted mass spectrometry analysis to confirm the presence and distribution of the modification. Based on the results, specific antibodies can then be developed, or follow-up ChIP experiments can be performed.
3. How should the relationship between histone modifications and gene expression be interpreted?
Creative Biogene not only provides histone modification profiling but can also integrate transcriptomic data (RNA-seq) for joint analysis, offering a comprehensive interpretation from modification patterns to gene expression changes.
4. Can this service be applied to drug development?
Yes. We have provided epigenetic drug discovery support for multiple pharmaceutical companies, including validation of HDAC and HMT inhibitors, as well as efficacy evaluation based on histone modification levels.
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